@jbrowse/plugin-linear-genome-view 3.3.0 → 3.5.0

package/dist/BaseLinearDisplay/models/BaseLinearDisplayModel.js

@@ -141,12 +141,28 @@ function stateModelFactory() {
         selectFeature(feature) {
             const session = (0, util_1.getSession)(self);
             if ((0, util_1.isSessionModelWithWidgets)(session)) {
-                const featureWidget = session.addWidget('BaseFeatureWidget', 'baseFeature', {
-                    view: (0, util_1.getContainingView)(self),
-                    track: (0, util_1.getContainingTrack)(self),
-                    featureData: feature.toJSON(),
-                });
-                session.showWidget(featureWidget);
+                const { rpcManager } = session;
+                const sessionId = (0, tracks_1.getRpcSessionId)(self);
+                const track = (0, util_1.getContainingTrack)(self);
+                const view = (0, util_1.getContainingView)(self);
+                const adapterConfig = (0, configuration_1.getConf)(track, 'adapter');
+                (async () => {
+                    try {
+                        const descriptions = await rpcManager.call(sessionId, 'CoreGetMetadata', {
+                            adapterConfig,
+                        });
+                        session.showWidget(session.addWidget('BaseFeatureWidget', 'baseFeature', {
+                            featureData: feature.toJSON(),
+                            view,
+                            track,
+                            descriptions,
+                        }));
+                    }
+                    catch (e) {
+                        console.error(e);
+                        (0, util_1.getSession)(e).notifyError(`${e}`, e);
+                    }
+                })();
             }
             if ((0, util_1.isSelectionContainer)(session)) {
                 session.setSelection(feature);

package/dist/LinearGenomeView/components/Cytobands.js

@@ -11,14 +11,14 @@ function rightRoundedRect(x, y, width, height, radius) {
 function leftRoundedRect(x, y, width, height, radius) {
     return `M${x + radius},${y}h${width - radius}v${height}h${radius - width}a${radius},${radius} 0 0 1 ${-radius},${-radius}v${2 * radius - height}a${radius},${radius} 0 0 1 ${radius},${-radius}z`;
 }
-function leftTriangle(x, y, width, height) {
+function leftTriangle(x, _y, width, height) {
     return [
         [x, 0],
         [x + width, height / 2],
         [x, height],
     ].toString();
 }
-function rightTriangle(x, y, width, height) {
+function rightTriangle(x, _y, width, height) {
     return [
         [x, height / 2],
         [x + width, 0],
@@ -42,14 +42,28 @@ const Cytobands = (0, mobx_react_1.observer)(function ({ overview, block, assemb
     const rcap = reversed ? 0 : cytobands.length - 1;
     const h = consts_1.HEADER_OVERVIEW_HEIGHT;
     let centromereSeen = false;
+    let curr = '';
+    let idx = 0;
     return ((0, jsx_runtime_1.jsx)("g", { transform: `translate(-${offsetPx})`, children: cytobands.map((args, index) => {
             const k = JSON.stringify(args);
-            const { refName, type, start, end } = args;
+            const { refName, name, type, start, end } = args;
             const s = overview.bpToPx({ refName, coord: start }) || 0;
             const e = overview.bpToPx({ refName, coord: end }) || 0;
             const l = Math.min(s, e);
             const w = Math.abs(e - s);
-            const c = colorMap[type] || 'black';
+            if (type === 'n/a') {
+                const match = name === null || name === void 0 ? void 0 : name.match(/^(\d+)([A-Za-z])/);
+                const ret = match[1] + match[2];
+                if (ret && ret !== curr) {
+                    curr = ret;
+                    idx++;
+                }
+            }
+            const c = type === 'n/a'
+                ? idx % 2
+                    ? 'black'
+                    : '#a77'
+                : colorMap[type] || 'black';
             if (type === 'acen' && !centromereSeen) {
                 centromereSeen = true;
                 return ((0, jsx_runtime_1.jsx)("polygon", { points: reversed

package/dist/LinearGenomeView/components/GetSequenceDialog.js

@@ -33,8 +33,9 @@ async function fetchSequence(model, regions) {
     if (!leftOffset || !rightOffset) {
         throw new Error('no offsets on model to use for range');
     }
-    if (leftOffset.assemblyName !== rightOffset.assemblyName) {
-        throw new Error('not able to fetch sequences from multiple assemblies');
+    const assemblyNames = new Set(regions.map(r => r.assemblyName));
+    if (assemblyNames.size > 1) {
+        throw new Error('not able to fetch sequences from multiple assemblies currently');
     }
     const { rpcManager, assemblyManager } = session;
     const assemblyName = leftOffset.assemblyName || rightOffset.assemblyName || '';

package/dist/LinearGenomeView/components/HeaderPanControls.js

@@ -16,9 +16,6 @@ const useStyles = (0, mui_1.makeStyles)()(theme => ({
         color: theme.palette.text.primary,
         margin: consts_1.SPACING,
     },
-    buttonSpacer: {
-        marginRight: theme.spacing(2),
-    },
 }));
 function HeaderPanControls({ model }) {
     const { classes } = useStyles();

package/dist/LinearGenomeView/components/MiniControls.js

@@ -17,6 +17,7 @@ const useStyles = (0, mui_1.makeStyles)()(theme => ({
         position: 'absolute',
         right: 0,
         background: theme.palette.background.paper,
+        zIndex: 2,
     },
     focusedBackground: {
         background: (0, material_1.alpha)(theme.palette.secondary.light, 0.2),

package/dist/LinearGenomeView/components/OverviewRubberband.js

@@ -17,12 +17,6 @@ const useStyles = (0, mui_1.makeStyles)()({
         width: '100%',
         minHeight: 8,
     },
-    guide: {
-        pointerEvents: 'none',
-        height: '100%',
-        width: 1,
-        position: 'absolute',
-    },
     rel: {
         position: 'relative',
     },

package/dist/LinearGenomeView/components/OverviewRubberbandHoverTooltip.js

@@ -6,20 +6,12 @@ const material_1 = require("@mui/material");
 const mobx_react_1 = require("mobx-react");
 const mui_1 = require("tss-react/mui");
 const useStyles = (0, mui_1.makeStyles)()({
-    rubberbandControl: {
-        cursor: 'crosshair',
-        width: '100%',
-        minHeight: 8,
-    },
     guide: {
         pointerEvents: 'none',
         height: '100%',
         width: 1,
         position: 'absolute',
     },
-    rel: {
-        position: 'relative',
-    },
 });
 const OverviewRubberbandHoverTooltip = (0, mobx_react_1.observer)(function ({ model, open, guideX, overview, }) {
     var _a;
@@ -31,6 +23,6 @@ const OverviewRubberbandHoverTooltip = (0, mobx_react_1.observer)(function ({ mo
     const cytoband = (_a = assembly === null || assembly === void 0 ? void 0 : assembly.cytobands) === null || _a === void 0 ? void 0 : _a.find(f => px.coord > f.get('start') &&
         px.coord < f.get('end') &&
         px.refName === assembly.getCanonicalRefName(f.get('refName')));
-    return ((0, jsx_runtime_1.jsx)(material_1.Tooltip, { open: open, placement: "top", title: [(0, util_1.stringify)(px), cytoband === null || cytoband === void 0 ? void 0 : cytoband.get('name')].join(' '), arrow: true, children: (0, jsx_runtime_1.jsx)("div", { className: classes.guide, style: { left: guideX } }) }));
+    return ((0, jsx_runtime_1.jsx)(material_1.Tooltip, { open: open, placement: "top", title: [(0, util_1.stringify)(px), cytoband === null || cytoband === void 0 ? void 0 : cytoband.get('name'), cytoband === null || cytoband === void 0 ? void 0 : cytoband.get('type')].join(' '), arrow: true, children: (0, jsx_runtime_1.jsx)("div", { className: classes.guide, style: { left: guideX } }) }));
 });
 exports.default = OverviewRubberbandHoverTooltip;

package/dist/LinearGenomeView/components/RefNameAutocomplete/index.js

@@ -63,27 +63,31 @@ const RefNameAutocomplete = (0, mobx_react_1.observer)(function ({ model, onSele
                     return;
                 }
                 setLoaded(false);
-                const results = await fetchResults(debouncedSearch);
-                setLoaded(true);
-                setSearchOptions((0, util_2.getDeduplicatedResult)(results));
+                setSearchOptions((0, util_2.getDeduplicatedResult)(await fetchResults(debouncedSearch)));
             }
             catch (e) {
                 console.error(e);
                 session.notifyError(`${e}`, e);
             }
+            finally {
+                setLoaded(true);
+            }
         })();
     }, [assemblyName, fetchResults, debouncedSearch, session]);
     const inputBoxVal = coarseVisibleLocStrings || value || '';
-    const width = Math.min(Math.max((0, util_1.measureText)(inputBoxVal, 14) + 100, minWidth), maxWidth);
-    const refNames = assembly === null || assembly === void 0 ? void 0 : assembly.refNames;
-    const regionOptions = (refNames === null || refNames === void 0 ? void 0 : refNames.map(refName => ({
+    const regions = assembly === null || assembly === void 0 ? void 0 : assembly.regions;
+    const regionOptions = (regions === null || regions === void 0 ? void 0 : regions.map(region => ({
         result: new BaseResults_1.RefSequenceResult({
-            refName,
-            label: refName,
+            refName: region.refName,
+            label: region.refName,
+            displayString: region.refName,
             matchedAttribute: 'refName',
         }),
     }))) || [];
-    return ((0, jsx_runtime_1.jsx)(material_1.Autocomplete, { "data-testid": "autocomplete", disableListWrap: true, disableClearable: true, disabled: !assemblyName, freeSolo: true, includeInputInList: true, selectOnFocus: true, style: { ...style, width }, value: inputBoxVal, loading: !loaded, inputValue: inputValue, onInputChange: (_event, newInputValue) => {
+    return ((0, jsx_runtime_1.jsx)(material_1.Autocomplete, { "data-testid": "autocomplete", disableListWrap: true, disableClearable: true, disabled: !assemblyName, freeSolo: true, includeInputInList: true, selectOnFocus: true, style: {
+            ...style,
+            width: Math.min(Math.max((0, util_1.measureText)(inputBoxVal, 14) + 100, minWidth), maxWidth),
+        }, value: inputBoxVal, loading: !loaded, inputValue: inputValue, onInputChange: (_event, newInputValue) => {
             setInputValue(newInputValue);
             onChange === null || onChange === void 0 ? void 0 : onChange(newInputValue);
         }, loadingText: "loading results", open: open, onOpen: () => {
@@ -100,7 +104,9 @@ const RefNameAutocomplete = (0, mobx_react_1.observer)(function ({ model, onSele
                 return;
             }
             if (typeof selectedOption === 'string') {
-                onSelect === null || onSelect === void 0 ? void 0 : onSelect(new BaseResults_1.default({ label: selectedOption }));
+                onSelect === null || onSelect === void 0 ? void 0 : onSelect(new BaseResults_1.default({
+                    label: selectedOption,
+                }));
             }
             else {
                 onSelect === null || onSelect === void 0 ? void 0 : onSelect(selectedOption.result);

package/dist/LinearGenomeView/components/SearchBox.d.ts

@@ -1,4 +1,4 @@
-import type { LinearGenomeViewModel } from '..';
+import type { LinearGenomeViewModel } from '../model';
 declare const SearchBox: ({ model, showHelp, }: {
     showHelp?: boolean;
     model: LinearGenomeViewModel;

package/dist/LinearGenomeView/components/SearchBox.js

@@ -13,11 +13,33 @@ const EndAdornment_1 = __importDefault(require("./RefNameAutocomplete/EndAdornme
 const util_2 = require("./util");
 const searchUtils_1 = require("../../searchUtils");
 const consts_1 = require("../consts");
-const useStyles = (0, mui_1.makeStyles)()(() => ({
+const useStyles = (0, mui_1.makeStyles)()({
     headerRefName: {
         minWidth: 100,
     },
-}));
+});
+async function onSelect({ option, model, assemblyName, }) {
+    var _a;
+    const { assemblyManager } = (0, util_1.getSession)(model);
+    const assembly = assemblyManager.get(assemblyName);
+    if (option.hasLocation()) {
+        await (0, searchUtils_1.navToOption)({
+            option,
+            model,
+            assemblyName,
+        });
+    }
+    else if ((_a = option.results) === null || _a === void 0 ? void 0 : _a.length) {
+        model.setSearchResults(option.results, option.getLabel());
+    }
+    else if (assembly) {
+        await (0, searchUtils_1.handleSelectedRegion)({
+            input: option.getLabel(),
+            assembly,
+            model,
+        });
+    }
+}
 const SearchBox = (0, mobx_react_1.observer)(function ({ model, showHelp = true, }) {
     const { classes } = useStyles();
     const theme = (0, material_1.useTheme)();
@@ -28,21 +50,12 @@ const SearchBox = (0, mobx_react_1.observer)(function ({ model, showHelp = true,
     const assembly = assemblyManager.get(assemblyName);
     const searchScope = model.searchScope(assemblyName);
     return ((0, jsx_runtime_1.jsx)(RefNameAutocomplete_1.default, { onSelect: async (option) => {
-            var _a;
             try {
-                if (option.hasLocation()) {
-                    await (0, searchUtils_1.navToOption)({ option, model, assemblyName });
-                }
-                else if ((_a = option.results) === null || _a === void 0 ? void 0 : _a.length) {
-                    model.setSearchResults(option.results, option.getLabel());
-                }
-                else if (assembly) {
-                    await (0, searchUtils_1.handleSelectedRegion)({
-                        input: option.getLabel(),
-                        assembly,
-                        model,
-                    });
-                }
+                await onSelect({
+                    model,
+                    assemblyName,
+                    option,
+                });
             }
             catch (e) {
                 console.error(e);

package/dist/LinearGenomeView/components/TrackLabel.js

@@ -17,6 +17,7 @@ const TrackLabelDragHandle_1 = __importDefault(require("./TrackLabelDragHandle")
 const TrackLabelMenu_1 = __importDefault(require("./TrackLabelMenu"));
 const useStyles = (0, mui_1.makeStyles)()(theme => ({
     root: {
+        zIndex: 200,
         background: (0, material_1.alpha)(theme.palette.background.paper, 0.8),
         '&:hover': {
             background: theme.palette.background.paper,

package/dist/LinearGenomeView/components/TrackLabelMenu.js

@@ -22,16 +22,9 @@ const TrackLabelMenu = (0, mobx_react_1.observer)(function ({ track, }) {
     const trackConf = track.configuration;
     const minimized = track.minimized;
     const pinned = track.pinned;
-    let lgvHasParentView;
-    try {
-        (0, util_1.getContainingView)(view);
-        lgvHasParentView = true;
-    }
-    catch (error) {
-        lgvHasParentView = false;
-    }
+    const { isTopLevelView } = view;
     const items = [
-        ...(lgvHasParentView
+        ...(isTopLevelView
             ? []
             : [
                 {

package/dist/LinearGenomeView/components/useWheelScroll.js

@@ -2,16 +2,27 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.useWheelScroll = useWheelScroll;
 const react_1 = require("react");
+const util_1 = require("@jbrowse/core/util");
 function useWheelScroll(ref, model) {
     const delta = (0, react_1.useRef)(0);
     const timeout = (0, react_1.useRef)(null);
     const scheduled = (0, react_1.useRef)(false);
     (0, react_1.useEffect)(() => {
+        let samples = [];
         const curr = ref.current;
         function onWheel(event) {
             if (event.ctrlKey) {
                 event.preventDefault();
-                delta.current += event.deltaY / 500;
+                samples.push(event.deltaY);
+                const averageDeltaY = Math.abs((0, util_1.sum)(samples)) / samples.length;
+                const normalizer = averageDeltaY < 6
+                    ? 25
+                    : averageDeltaY > 30
+                        ? averageDeltaY > 150
+                            ? 500
+                            : 150
+                        : 75;
+                delta.current += event.deltaY / normalizer;
                 model.setScaleFactor(delta.current < 0 ? 1 - delta.current : 1 / (1 + delta.current));
                 if (timeout.current) {
                     clearTimeout(timeout.current);
@@ -22,6 +33,7 @@ function useWheelScroll(ref, model) {
                         ? model.bpPerPx * (1 + delta.current)
                         : model.bpPerPx / (1 - delta.current), event.clientX - ((curr === null || curr === void 0 ? void 0 : curr.getBoundingClientRect().left) || 0));
                     delta.current = 0;
+                    samples = [];
                 }, 300);
             }
             else {

package/dist/LinearGenomeView/components/util.d.ts

@@ -21,4 +21,5 @@ export declare function getCytobands(assembly: Assembly | undefined, refName: st
     start: number;
     end: number;
     type: string;
+    name: any;
 }[];

package/dist/LinearGenomeView/components/util.js

@@ -14,12 +14,14 @@ async function fetchResults({ queryString, searchType, searchScope, rankSearchRe
     if (!textSearchManager) {
         console.warn('No text search manager');
     }
-    const textSearchResults = await (textSearchManager === null || textSearchManager === void 0 ? void 0 : textSearchManager.search({
+    const textSearchResults = (await (textSearchManager === null || textSearchManager === void 0 ? void 0 : textSearchManager.search({
         queryString,
         searchType,
-    }, searchScope, rankSearchResults));
-    const refNameResults = (_a = assembly === null || assembly === void 0 ? void 0 : assembly.allRefNames) === null || _a === void 0 ? void 0 : _a.filter(ref => ref.toLowerCase().startsWith(queryString.toLowerCase())).slice(0, 10).map(r => new BaseResults_1.default({ label: r }));
-    return (0, util_1.dedupe)([...(refNameResults || []), ...(textSearchResults || [])], elt => elt.getId());
+    }, searchScope, rankSearchResults))) || [];
+    const refNameResults = ((_a = assembly === null || assembly === void 0 ? void 0 : assembly.allRefNames) === null || _a === void 0 ? void 0 : _a.filter(ref => ref.toLowerCase().startsWith(queryString.toLowerCase())).slice(0, 10).map(r => new BaseResults_1.default({
+        label: r,
+    }))) || [];
+    return (0, util_1.dedupe)([...refNameResults, ...textSearchResults], elt => elt.getId());
 }
 function splitLast(str, split) {
     const lastIndex = str.lastIndexOf(split);
@@ -42,5 +44,6 @@ function getCytobands(assembly, refName) {
         start: f.get('start'),
         end: f.get('end'),
         type: f.get('gieStain'),
+        name: f.get('name'),
     })).filter(f => f.refName === refName)) || []);
 }

package/dist/LinearGenomeView/model.d.ts

@@ -58,7 +58,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     readonly width: number;
     readonly interRegionPaddingWidth: number;
     readonly assemblyNames: string[];
-    readonly stickyViewHeaders: boolean;
+    readonly isTopLevelView: import("@jbrowse/core/util").AbstractViewModel | undefined;
+    readonly stickyViewHeaders: boolean | undefined;
     readonly rubberbandTop: number;
     readonly pinnedTracksTop: number;
 } & {
@@ -169,13 +170,13 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     setCoarseDynamicBlocks(blocks: BlockSet): void;
 } & {
     moveTo(start?: BpOffset, end?: BpOffset): void;
-    navToLocString(input: string, optAssemblyName?: string): Promise<void>;
+    navToLocString(input: string, optAssemblyName?: string, grow?: number): Promise<void>;
     navToSearchString({ input, assembly, }: {
         input: string;
         assembly: Assembly;
     }): Promise<void>;
-    navToLocation(parsedLocString: ParsedLocString, assemblyName?: string): Promise<void>;
-    navToLocations(parsedLocStrings: ParsedLocString[], assemblyName?: string): Promise<void>;
+    navToLocation(parsedLocString: ParsedLocString, assemblyName?: string, grow?: number): Promise<void>;
+    navToLocations(regions: ParsedLocString[], assemblyName?: string, grow?: number): Promise<void>;
     navTo(query: NavLocation): void;
     navToMultiple(locations: NavLocation[]): void;
 } & {
@@ -243,9 +244,9 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     displayName: string | undefined;
     tracks: any[];
     minimized: boolean;
-    displayedRegions: Region[];
     offsetPx: number;
     bpPerPx: number;
+    displayedRegions: Region[];
     hideHeader: boolean;
     hideHeaderOverview: boolean;
     hideNoTracksActive: boolean;

package/dist/LinearGenomeView/model.js

@@ -136,10 +136,14 @@ function stateModelFactory(pluginManager) {
                 ...new Set(self.displayedRegions.map(region => region.assemblyName)),
             ];
         },
+        get isTopLevelView() {
+            const session = (0, util_1.getSession)(self);
+            return session.views.find(r => r.id === self.id);
+        },
         get stickyViewHeaders() {
             const session = (0, util_1.getSession)(self);
             return (0, product_core_1.isSessionWithMultipleViews)(session)
-                ? session.stickyViewHeaders
+                ? this.isTopLevelView && session.stickyViewHeaders
                 : false;
         },
         get rubberbandTop() {
@@ -262,12 +266,6 @@ function stateModelFactory(pluginManager) {
             return self.tracks.find(t => t.configuration.trackId === id);
         },
         rankSearchResults(results) {
-            const openTrackIds = new Set(self.tracks.map(track => track.configuration.trackId));
-            for (const result of results) {
-                if (openTrackIds.has(result.trackId)) {
-                    result.updateScore(result.getScore() + 1);
-                }
-            }
             return results;
         },
         rewriteOnClicks(trackType, viewMenuActions) {
@@ -840,14 +838,14 @@ function stateModelFactory(pluginManager) {
         moveTo(start, end) {
             (0, Base1DUtils_1.moveTo)(self, start, end);
         },
-        async navToLocString(input, optAssemblyName) {
+        async navToLocString(input, optAssemblyName, grow) {
             const { assemblyNames } = self;
             const { assemblyManager } = (0, util_1.getSession)(self);
             const assemblyName = optAssemblyName || assemblyNames[0];
             if (assemblyName) {
                 await assemblyManager.waitForAssembly(assemblyName);
             }
-            return this.navToLocations((0, util_2.parseLocStrings)(input, assemblyName, (ref, asm) => assemblyManager.isValidRefName(ref, asm)), assemblyName);
+            return this.navToLocations((0, util_2.parseLocStrings)(input, assemblyName, (ref, asm) => assemblyManager.isValidRefName(ref, asm)), assemblyName, grow);
         },
         async navToSearchString({ input, assembly, }) {
             await (0, searchUtils_1.handleSelectedRegion)({
@@ -856,13 +854,18 @@ function stateModelFactory(pluginManager) {
                 model: self,
             });
         },
-        async navToLocation(parsedLocString, assemblyName) {
-            return this.navToLocations([parsedLocString], assemblyName);
+        async navToLocation(parsedLocString, assemblyName, grow) {
+            return this.navToLocations([parsedLocString], assemblyName, grow);
         },
-        async navToLocations(parsedLocStrings, assemblyName) {
+        async navToLocations(regions, assemblyName, grow) {
             const { assemblyManager } = (0, util_1.getSession)(self);
             await (0, mobx_1.when)(() => self.volatileWidth !== undefined);
-            const locations = await (0, util_2.generateLocations)(parsedLocStrings, assemblyManager, assemblyName);
+            const locations = await (0, util_2.generateLocations)({
+                regions,
+                assemblyManager,
+                assemblyName,
+                grow,
+            });
             if (locations.length === 1) {
                 const loc = locations[0];
                 const { reversed, parentRegion, start, end } = loc;

package/dist/LinearGenomeView/util.d.ts

@@ -9,7 +9,12 @@ export declare function makeTicks(start: number, end: number, bpPerPx: number, e
     base: number;
     index: number;
 }[];
-export declare function generateLocations(regions: ParsedLocString[], assemblyManager: AssemblyManager, assemblyName?: string): Promise<{
+export declare function generateLocations({ regions, assemblyManager, assemblyName, grow, }: {
+    regions: ParsedLocString[];
+    assemblyManager: AssemblyManager;
+    assemblyName?: string;
+    grow?: number;
+}): Promise<{
     assemblyName: string;
     parentRegion: import("@jbrowse/core/assemblyManager/assembly").BasicRegion;
     end?: number | undefined;

package/dist/LinearGenomeView/util.js

@@ -57,7 +57,7 @@ function makeTicks(start, end, bpPerPx, emitMajor = true, emitMinor = true) {
     }
     return ticks;
 }
-async function generateLocations(regions, assemblyManager, assemblyName) {
+async function generateLocations({ regions, assemblyManager, assemblyName, grow, }) {
     return Promise.all(regions.map(async (region) => {
         const asmName = region.assemblyName || assemblyName;
         if (!asmName) {
@@ -80,11 +80,25 @@ async function generateLocations(regions, assemblyManager, assemblyName) {
         if (!parentRegion) {
             throw new Error(`Could not find refName ${refName} in ${asmName}`);
         }
-        return {
-            ...region,
-            assemblyName: asmName,
-            parentRegion,
-        };
+        const { start, end } = region;
+        if (grow && start && end) {
+            const len = end - start;
+            const margin = len * grow;
+            return {
+                ...region,
+                start: Math.max(0, start - margin),
+                end: end + margin,
+                assemblyName: asmName,
+                parentRegion,
+            };
+        }
+        else {
+            return {
+                ...region,
+                assemblyName: asmName,
+                parentRegion,
+            };
+        }
     }));
 }
 function parseLocStrings(input, assemblyName, isValidRefName) {

package/dist/searchUtils.js

@@ -14,7 +14,7 @@ async function navToOption({ option, model, assemblyName, }) {
     const location = option.getLocation();
     const trackId = option.getTrackId();
     if (location) {
-        await model.navToLocString(location, assemblyName);
+        await model.navToLocString(location, assemblyName, 0.2);
         if (trackId) {
             model.showTrack(trackId);
         }

package/esm/BaseLinearDisplay/models/BaseLinearDisplayModel.js

@@ -1,9 +1,9 @@
 import { lazy } from 'react';
-import { ConfigurationReference } from '@jbrowse/core/configuration';
+import { ConfigurationReference, getConf } from '@jbrowse/core/configuration';
 import { BaseDisplay } from '@jbrowse/core/pluggableElementTypes/models';
 import { getContainingTrack, getContainingView, getSession, isFeature, isSelectionContainer, isSessionModelWithWidgets, } from '@jbrowse/core/util';
 import CompositeMap from '@jbrowse/core/util/compositeMap';
-import { getParentRenderProps } from '@jbrowse/core/util/tracks';
+import { getParentRenderProps, getRpcSessionId, } from '@jbrowse/core/util/tracks';
 import CenterFocusStrongIcon from '@mui/icons-material/CenterFocusStrong';
 import MenuOpenIcon from '@mui/icons-material/MenuOpen';
 import { autorun } from 'mobx';
@@ -102,12 +102,28 @@ function stateModelFactory() {
         selectFeature(feature) {
             const session = getSession(self);
             if (isSessionModelWithWidgets(session)) {
-                const featureWidget = session.addWidget('BaseFeatureWidget', 'baseFeature', {
-                    view: getContainingView(self),
-                    track: getContainingTrack(self),
-                    featureData: feature.toJSON(),
-                });
-                session.showWidget(featureWidget);
+                const { rpcManager } = session;
+                const sessionId = getRpcSessionId(self);
+                const track = getContainingTrack(self);
+                const view = getContainingView(self);
+                const adapterConfig = getConf(track, 'adapter');
+                (async () => {
+                    try {
+                        const descriptions = await rpcManager.call(sessionId, 'CoreGetMetadata', {
+                            adapterConfig,
+                        });
+                        session.showWidget(session.addWidget('BaseFeatureWidget', 'baseFeature', {
+                            featureData: feature.toJSON(),
+                            view,
+                            track,
+                            descriptions,
+                        }));
+                    }
+                    catch (e) {
+                        console.error(e);
+                        getSession(e).notifyError(`${e}`, e);
+                    }
+                })();
             }
             if (isSelectionContainer(session)) {
                 session.setSelection(feature);

package/esm/LinearGenomeView/components/Cytobands.js

@@ -9,14 +9,14 @@ function rightRoundedRect(x, y, width, height, radius) {
 function leftRoundedRect(x, y, width, height, radius) {
     return `M${x + radius},${y}h${width - radius}v${height}h${radius - width}a${radius},${radius} 0 0 1 ${-radius},${-radius}v${2 * radius - height}a${radius},${radius} 0 0 1 ${radius},${-radius}z`;
 }
-function leftTriangle(x, y, width, height) {
+function leftTriangle(x, _y, width, height) {
     return [
         [x, 0],
         [x + width, height / 2],
         [x, height],
     ].toString();
 }
-function rightTriangle(x, y, width, height) {
+function rightTriangle(x, _y, width, height) {
     return [
         [x, height / 2],
         [x + width, 0],
@@ -40,14 +40,28 @@ const Cytobands = observer(function ({ overview, block, assembly, }) {
     const rcap = reversed ? 0 : cytobands.length - 1;
     const h = HEADER_OVERVIEW_HEIGHT;
     let centromereSeen = false;
+    let curr = '';
+    let idx = 0;
     return (_jsx("g", { transform: `translate(-${offsetPx})`, children: cytobands.map((args, index) => {
             const k = JSON.stringify(args);
-            const { refName, type, start, end } = args;
+            const { refName, name, type, start, end } = args;
             const s = overview.bpToPx({ refName, coord: start }) || 0;
             const e = overview.bpToPx({ refName, coord: end }) || 0;
             const l = Math.min(s, e);
             const w = Math.abs(e - s);
-            const c = colorMap[type] || 'black';
+            if (type === 'n/a') {
+                const match = name === null || name === void 0 ? void 0 : name.match(/^(\d+)([A-Za-z])/);
+                const ret = match[1] + match[2];
+                if (ret && ret !== curr) {
+                    curr = ret;
+                    idx++;
+                }
+            }
+            const c = type === 'n/a'
+                ? idx % 2
+                    ? 'black'
+                    : '#a77'
+                : colorMap[type] || 'black';
             if (type === 'acen' && !centromereSeen) {
                 centromereSeen = true;
                 return (_jsx("polygon", { points: reversed

package/esm/LinearGenomeView/components/GetSequenceDialog.js

@@ -28,8 +28,9 @@ async function fetchSequence(model, regions) {
     if (!leftOffset || !rightOffset) {
         throw new Error('no offsets on model to use for range');
     }
-    if (leftOffset.assemblyName !== rightOffset.assemblyName) {
-        throw new Error('not able to fetch sequences from multiple assemblies');
+    const assemblyNames = new Set(regions.map(r => r.assemblyName));
+    if (assemblyNames.size > 1) {
+        throw new Error('not able to fetch sequences from multiple assemblies currently');
     }
     const { rpcManager, assemblyManager } = session;
     const assemblyName = leftOffset.assemblyName || rightOffset.assemblyName || '';

package/esm/LinearGenomeView/components/HeaderPanControls.js

@@ -10,9 +10,6 @@ const useStyles = makeStyles()(theme => ({
         color: theme.palette.text.primary,
         margin: SPACING,
     },
-    buttonSpacer: {
-        marginRight: theme.spacing(2),
-    },
 }));
 export default function HeaderPanControls({ model }) {
     const { classes } = useStyles();

package/esm/LinearGenomeView/components/MiniControls.js

@@ -12,6 +12,7 @@ const useStyles = makeStyles()(theme => ({
         position: 'absolute',
         right: 0,
         background: theme.palette.background.paper,
+        zIndex: 2,
     },
     focusedBackground: {
         background: alpha(theme.palette.secondary.light, 0.2),

package/esm/LinearGenomeView/components/OverviewRubberband.js

@@ -12,12 +12,6 @@ const useStyles = makeStyles()({
         width: '100%',
         minHeight: 8,
     },
-    guide: {
-        pointerEvents: 'none',
-        height: '100%',
-        width: 1,
-        position: 'absolute',
-    },
     rel: {
         position: 'relative',
     },

package/esm/LinearGenomeView/components/OverviewRubberbandHoverTooltip.js

@@ -4,20 +4,12 @@ import { Tooltip } from '@mui/material';
 import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
 const useStyles = makeStyles()({
-    rubberbandControl: {
-        cursor: 'crosshair',
-        width: '100%',
-        minHeight: 8,
-    },
     guide: {
         pointerEvents: 'none',
         height: '100%',
         width: 1,
         position: 'absolute',
     },
-    rel: {
-        position: 'relative',
-    },
 });
 const OverviewRubberbandHoverTooltip = observer(function ({ model, open, guideX, overview, }) {
     var _a;
@@ -29,6 +21,6 @@ const OverviewRubberbandHoverTooltip = observer(function ({ model, open, guideX,
     const cytoband = (_a = assembly === null || assembly === void 0 ? void 0 : assembly.cytobands) === null || _a === void 0 ? void 0 : _a.find(f => px.coord > f.get('start') &&
         px.coord < f.get('end') &&
         px.refName === assembly.getCanonicalRefName(f.get('refName')));
-    return (_jsx(Tooltip, { open: open, placement: "top", title: [stringify(px), cytoband === null || cytoband === void 0 ? void 0 : cytoband.get('name')].join(' '), arrow: true, children: _jsx("div", { className: classes.guide, style: { left: guideX } }) }));
+    return (_jsx(Tooltip, { open: open, placement: "top", title: [stringify(px), cytoband === null || cytoband === void 0 ? void 0 : cytoband.get('name'), cytoband === null || cytoband === void 0 ? void 0 : cytoband.get('type')].join(' '), arrow: true, children: _jsx("div", { className: classes.guide, style: { left: guideX } }) }));
 });
 export default OverviewRubberbandHoverTooltip;

package/esm/LinearGenomeView/components/RefNameAutocomplete/index.js

@@ -25,27 +25,31 @@ const RefNameAutocomplete = observer(function ({ model, onSelect, assemblyName,
                     return;
                 }
                 setLoaded(false);
-                const results = await fetchResults(debouncedSearch);
-                setLoaded(true);
-                setSearchOptions(getDeduplicatedResult(results));
+                setSearchOptions(getDeduplicatedResult(await fetchResults(debouncedSearch)));
             }
             catch (e) {
                 console.error(e);
                 session.notifyError(`${e}`, e);
             }
+            finally {
+                setLoaded(true);
+            }
         })();
     }, [assemblyName, fetchResults, debouncedSearch, session]);
     const inputBoxVal = coarseVisibleLocStrings || value || '';
-    const width = Math.min(Math.max(measureText(inputBoxVal, 14) + 100, minWidth), maxWidth);
-    const refNames = assembly === null || assembly === void 0 ? void 0 : assembly.refNames;
-    const regionOptions = (refNames === null || refNames === void 0 ? void 0 : refNames.map(refName => ({
+    const regions = assembly === null || assembly === void 0 ? void 0 : assembly.regions;
+    const regionOptions = (regions === null || regions === void 0 ? void 0 : regions.map(region => ({
         result: new RefSequenceResult({
-            refName,
-            label: refName,
+            refName: region.refName,
+            label: region.refName,
+            displayString: region.refName,
             matchedAttribute: 'refName',
         }),
     }))) || [];
-    return (_jsx(Autocomplete, { "data-testid": "autocomplete", disableListWrap: true, disableClearable: true, disabled: !assemblyName, freeSolo: true, includeInputInList: true, selectOnFocus: true, style: { ...style, width }, value: inputBoxVal, loading: !loaded, inputValue: inputValue, onInputChange: (_event, newInputValue) => {
+    return (_jsx(Autocomplete, { "data-testid": "autocomplete", disableListWrap: true, disableClearable: true, disabled: !assemblyName, freeSolo: true, includeInputInList: true, selectOnFocus: true, style: {
+            ...style,
+            width: Math.min(Math.max(measureText(inputBoxVal, 14) + 100, minWidth), maxWidth),
+        }, value: inputBoxVal, loading: !loaded, inputValue: inputValue, onInputChange: (_event, newInputValue) => {
             setInputValue(newInputValue);
             onChange === null || onChange === void 0 ? void 0 : onChange(newInputValue);
         }, loadingText: "loading results", open: open, onOpen: () => {
@@ -62,7 +66,9 @@ const RefNameAutocomplete = observer(function ({ model, onSelect, assemblyName,
                 return;
             }
             if (typeof selectedOption === 'string') {
-                onSelect === null || onSelect === void 0 ? void 0 : onSelect(new BaseResult({ label: selectedOption }));
+                onSelect === null || onSelect === void 0 ? void 0 : onSelect(new BaseResult({
+                    label: selectedOption,
+                }));
             }
             else {
                 onSelect === null || onSelect === void 0 ? void 0 : onSelect(selectedOption.result);

package/esm/LinearGenomeView/components/SearchBox.d.ts

@@ -1,4 +1,4 @@
-import type { LinearGenomeViewModel } from '..';
+import type { LinearGenomeViewModel } from '../model';
 declare const SearchBox: ({ model, showHelp, }: {
     showHelp?: boolean;
     model: LinearGenomeViewModel;

package/esm/LinearGenomeView/components/SearchBox.js

@@ -8,11 +8,33 @@ import EndAdornment from './RefNameAutocomplete/EndAdornment';
 import { fetchResults } from './util';
 import { handleSelectedRegion, navToOption } from '../../searchUtils';
 import { SPACING, WIDGET_HEIGHT } from '../consts';
-const useStyles = makeStyles()(() => ({
+const useStyles = makeStyles()({
     headerRefName: {
         minWidth: 100,
     },
-}));
+});
+async function onSelect({ option, model, assemblyName, }) {
+    var _a;
+    const { assemblyManager } = getSession(model);
+    const assembly = assemblyManager.get(assemblyName);
+    if (option.hasLocation()) {
+        await navToOption({
+            option,
+            model,
+            assemblyName,
+        });
+    }
+    else if ((_a = option.results) === null || _a === void 0 ? void 0 : _a.length) {
+        model.setSearchResults(option.results, option.getLabel());
+    }
+    else if (assembly) {
+        await handleSelectedRegion({
+            input: option.getLabel(),
+            assembly,
+            model,
+        });
+    }
+}
 const SearchBox = observer(function ({ model, showHelp = true, }) {
     const { classes } = useStyles();
     const theme = useTheme();
@@ -23,21 +45,12 @@ const SearchBox = observer(function ({ model, showHelp = true, }) {
     const assembly = assemblyManager.get(assemblyName);
     const searchScope = model.searchScope(assemblyName);
     return (_jsx(RefNameAutocomplete, { onSelect: async (option) => {
-            var _a;
             try {
-                if (option.hasLocation()) {
-                    await navToOption({ option, model, assemblyName });
-                }
-                else if ((_a = option.results) === null || _a === void 0 ? void 0 : _a.length) {
-                    model.setSearchResults(option.results, option.getLabel());
-                }
-                else if (assembly) {
-                    await handleSelectedRegion({
-                        input: option.getLabel(),
-                        assembly,
-                        model,
-                    });
-                }
+                await onSelect({
+                    model,
+                    assemblyName,
+                    option,
+                });
             }
             catch (e) {
                 console.error(e);

package/esm/LinearGenomeView/components/TrackLabel.js

@@ -12,6 +12,7 @@ import TrackLabelDragHandle from './TrackLabelDragHandle';
 import TrackLabelMenu from './TrackLabelMenu';
 const useStyles = makeStyles()(theme => ({
     root: {
+        zIndex: 200,
         background: alpha(theme.palette.background.paper, 0.8),
         '&:hover': {
             background: theme.palette.background.paper,

package/esm/LinearGenomeView/components/TrackLabelMenu.js

@@ -17,16 +17,9 @@ const TrackLabelMenu = observer(function ({ track, }) {
     const trackConf = track.configuration;
     const minimized = track.minimized;
     const pinned = track.pinned;
-    let lgvHasParentView;
-    try {
-        getContainingView(view);
-        lgvHasParentView = true;
-    }
-    catch (error) {
-        lgvHasParentView = false;
-    }
+    const { isTopLevelView } = view;
     const items = [
-        ...(lgvHasParentView
+        ...(isTopLevelView
             ? []
             : [
                 {

package/esm/LinearGenomeView/components/useWheelScroll.js

@@ -1,14 +1,25 @@
 import { useEffect, useRef } from 'react';
+import { sum } from '@jbrowse/core/util';
 export function useWheelScroll(ref, model) {
     const delta = useRef(0);
     const timeout = useRef(null);
     const scheduled = useRef(false);
     useEffect(() => {
+        let samples = [];
         const curr = ref.current;
         function onWheel(event) {
             if (event.ctrlKey) {
                 event.preventDefault();
-                delta.current += event.deltaY / 500;
+                samples.push(event.deltaY);
+                const averageDeltaY = Math.abs(sum(samples)) / samples.length;
+                const normalizer = averageDeltaY < 6
+                    ? 25
+                    : averageDeltaY > 30
+                        ? averageDeltaY > 150
+                            ? 500
+                            : 150
+                        : 75;
+                delta.current += event.deltaY / normalizer;
                 model.setScaleFactor(delta.current < 0 ? 1 - delta.current : 1 / (1 + delta.current));
                 if (timeout.current) {
                     clearTimeout(timeout.current);
@@ -19,6 +30,7 @@ export function useWheelScroll(ref, model) {
                         ? model.bpPerPx * (1 + delta.current)
                         : model.bpPerPx / (1 - delta.current), event.clientX - ((curr === null || curr === void 0 ? void 0 : curr.getBoundingClientRect().left) || 0));
                     delta.current = 0;
+                    samples = [];
                 }, 300);
             }
             else {

package/esm/LinearGenomeView/components/util.d.ts

@@ -21,4 +21,5 @@ export declare function getCytobands(assembly: Assembly | undefined, refName: st
     start: number;
     end: number;
     type: string;
+    name: any;
 }[];

package/esm/LinearGenomeView/components/util.js

@@ -5,12 +5,14 @@ export async function fetchResults({ queryString, searchType, searchScope, rankS
     if (!textSearchManager) {
         console.warn('No text search manager');
     }
-    const textSearchResults = await (textSearchManager === null || textSearchManager === void 0 ? void 0 : textSearchManager.search({
+    const textSearchResults = (await (textSearchManager === null || textSearchManager === void 0 ? void 0 : textSearchManager.search({
         queryString,
         searchType,
-    }, searchScope, rankSearchResults));
-    const refNameResults = (_a = assembly === null || assembly === void 0 ? void 0 : assembly.allRefNames) === null || _a === void 0 ? void 0 : _a.filter(ref => ref.toLowerCase().startsWith(queryString.toLowerCase())).slice(0, 10).map(r => new BaseResult({ label: r }));
-    return dedupe([...(refNameResults || []), ...(textSearchResults || [])], elt => elt.getId());
+    }, searchScope, rankSearchResults))) || [];
+    const refNameResults = ((_a = assembly === null || assembly === void 0 ? void 0 : assembly.allRefNames) === null || _a === void 0 ? void 0 : _a.filter(ref => ref.toLowerCase().startsWith(queryString.toLowerCase())).slice(0, 10).map(r => new BaseResult({
+        label: r,
+    }))) || [];
+    return dedupe([...refNameResults, ...textSearchResults], elt => elt.getId());
 }
 export function splitLast(str, split) {
     const lastIndex = str.lastIndexOf(split);
@@ -33,5 +35,6 @@ export function getCytobands(assembly, refName) {
         start: f.get('start'),
         end: f.get('end'),
         type: f.get('gieStain'),
+        name: f.get('name'),
     })).filter(f => f.refName === refName)) || []);
 }

package/esm/LinearGenomeView/model.d.ts

@@ -58,7 +58,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     readonly width: number;
     readonly interRegionPaddingWidth: number;
     readonly assemblyNames: string[];
-    readonly stickyViewHeaders: boolean;
+    readonly isTopLevelView: import("@jbrowse/core/util").AbstractViewModel | undefined;
+    readonly stickyViewHeaders: boolean | undefined;
     readonly rubberbandTop: number;
     readonly pinnedTracksTop: number;
 } & {
@@ -169,13 +170,13 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     setCoarseDynamicBlocks(blocks: BlockSet): void;
 } & {
     moveTo(start?: BpOffset, end?: BpOffset): void;
-    navToLocString(input: string, optAssemblyName?: string): Promise<void>;
+    navToLocString(input: string, optAssemblyName?: string, grow?: number): Promise<void>;
     navToSearchString({ input, assembly, }: {
         input: string;
         assembly: Assembly;
     }): Promise<void>;
-    navToLocation(parsedLocString: ParsedLocString, assemblyName?: string): Promise<void>;
-    navToLocations(parsedLocStrings: ParsedLocString[], assemblyName?: string): Promise<void>;
+    navToLocation(parsedLocString: ParsedLocString, assemblyName?: string, grow?: number): Promise<void>;
+    navToLocations(regions: ParsedLocString[], assemblyName?: string, grow?: number): Promise<void>;
     navTo(query: NavLocation): void;
     navToMultiple(locations: NavLocation[]): void;
 } & {
@@ -243,9 +244,9 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     displayName: string | undefined;
     tracks: any[];
     minimized: boolean;
-    displayedRegions: Region[];
     offsetPx: number;
     bpPerPx: number;
+    displayedRegions: Region[];
     hideHeader: boolean;
     hideHeaderOverview: boolean;
     hideNoTracksActive: boolean;

package/esm/LinearGenomeView/model.js

@@ -96,10 +96,14 @@ export function stateModelFactory(pluginManager) {
                 ...new Set(self.displayedRegions.map(region => region.assemblyName)),
             ];
         },
+        get isTopLevelView() {
+            const session = getSession(self);
+            return session.views.find(r => r.id === self.id);
+        },
         get stickyViewHeaders() {
             const session = getSession(self);
             return isSessionWithMultipleViews(session)
-                ? session.stickyViewHeaders
+                ? this.isTopLevelView && session.stickyViewHeaders
                 : false;
         },
         get rubberbandTop() {
@@ -222,12 +226,6 @@ export function stateModelFactory(pluginManager) {
             return self.tracks.find(t => t.configuration.trackId === id);
         },
         rankSearchResults(results) {
-            const openTrackIds = new Set(self.tracks.map(track => track.configuration.trackId));
-            for (const result of results) {
-                if (openTrackIds.has(result.trackId)) {
-                    result.updateScore(result.getScore() + 1);
-                }
-            }
             return results;
         },
         rewriteOnClicks(trackType, viewMenuActions) {
@@ -800,14 +798,14 @@ export function stateModelFactory(pluginManager) {
         moveTo(start, end) {
             moveTo(self, start, end);
         },
-        async navToLocString(input, optAssemblyName) {
+        async navToLocString(input, optAssemblyName, grow) {
             const { assemblyNames } = self;
             const { assemblyManager } = getSession(self);
             const assemblyName = optAssemblyName || assemblyNames[0];
             if (assemblyName) {
                 await assemblyManager.waitForAssembly(assemblyName);
             }
-            return this.navToLocations(parseLocStrings(input, assemblyName, (ref, asm) => assemblyManager.isValidRefName(ref, asm)), assemblyName);
+            return this.navToLocations(parseLocStrings(input, assemblyName, (ref, asm) => assemblyManager.isValidRefName(ref, asm)), assemblyName, grow);
         },
         async navToSearchString({ input, assembly, }) {
             await handleSelectedRegion({
@@ -816,13 +814,18 @@ export function stateModelFactory(pluginManager) {
                 model: self,
             });
         },
-        async navToLocation(parsedLocString, assemblyName) {
-            return this.navToLocations([parsedLocString], assemblyName);
+        async navToLocation(parsedLocString, assemblyName, grow) {
+            return this.navToLocations([parsedLocString], assemblyName, grow);
         },
-        async navToLocations(parsedLocStrings, assemblyName) {
+        async navToLocations(regions, assemblyName, grow) {
             const { assemblyManager } = getSession(self);
             await when(() => self.volatileWidth !== undefined);
-            const locations = await generateLocations(parsedLocStrings, assemblyManager, assemblyName);
+            const locations = await generateLocations({
+                regions,
+                assemblyManager,
+                assemblyName,
+                grow,
+            });
             if (locations.length === 1) {
                 const loc = locations[0];
                 const { reversed, parentRegion, start, end } = loc;

package/esm/LinearGenomeView/util.d.ts

@@ -9,7 +9,12 @@ export declare function makeTicks(start: number, end: number, bpPerPx: number, e
     base: number;
     index: number;
 }[];
-export declare function generateLocations(regions: ParsedLocString[], assemblyManager: AssemblyManager, assemblyName?: string): Promise<{
+export declare function generateLocations({ regions, assemblyManager, assemblyName, grow, }: {
+    regions: ParsedLocString[];
+    assemblyManager: AssemblyManager;
+    assemblyName?: string;
+    grow?: number;
+}): Promise<{
     assemblyName: string;
     parentRegion: import("@jbrowse/core/assemblyManager/assembly").BasicRegion;
     end?: number | undefined;

package/esm/LinearGenomeView/util.js

@@ -50,7 +50,7 @@ export function makeTicks(start, end, bpPerPx, emitMajor = true, emitMinor = tru
     }
     return ticks;
 }
-export async function generateLocations(regions, assemblyManager, assemblyName) {
+export async function generateLocations({ regions, assemblyManager, assemblyName, grow, }) {
     return Promise.all(regions.map(async (region) => {
         const asmName = region.assemblyName || assemblyName;
         if (!asmName) {
@@ -73,11 +73,25 @@ export async function generateLocations(regions, assemblyManager, assemblyName)
         if (!parentRegion) {
             throw new Error(`Could not find refName ${refName} in ${asmName}`);
         }
-        return {
-            ...region,
-            assemblyName: asmName,
-            parentRegion,
-        };
+        const { start, end } = region;
+        if (grow && start && end) {
+            const len = end - start;
+            const margin = len * grow;
+            return {
+                ...region,
+                start: Math.max(0, start - margin),
+                end: end + margin,
+                assemblyName: asmName,
+                parentRegion,
+            };
+        }
+        else {
+            return {
+                ...region,
+                assemblyName: asmName,
+                parentRegion,
+            };
+        }
     }));
 }
 export function parseLocStrings(input, assemblyName, isValidRefName) {

package/esm/searchUtils.js

@@ -4,7 +4,7 @@ export async function navToOption({ option, model, assemblyName, }) {
     const location = option.getLocation();
     const trackId = option.getTrackId();
     if (location) {
-        await model.navToLocString(location, assemblyName);
+        await model.navToLocString(location, assemblyName, 0.2);
         if (trackId) {
             model.showTrack(trackId);
         }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-linear-genome-view",
-  "version": "3.3.0",
+  "version": "3.5.0",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
     "jbrowse",
@@ -38,7 +38,7 @@
     "useSrc": "node ../../scripts/useSrc.js"
   },
   "dependencies": {
-    "@jbrowse/core": "^3.3.0",
+    "@jbrowse/core": "^3.5.0",
     "@mui/icons-material": "^7.0.0",
     "@mui/material": "^7.0.0",
     "@types/file-saver": "^2.0.1",
@@ -58,5 +58,5 @@
     "access": "public"
   },
   "module": "esm/index.js",
-  "gitHead": "0bb64d8cc7ecdd167515308b31eec3d9acbc59e4"
+  "gitHead": "8a8aa0aab2229dece106a5715a767e649e2fe92b"
 }